LAMMPS (8 Feb 2023)
# QMMM with NWChem

units		real
atom_style	full

bond_style      harmonic
angle_style     harmonic

read_data       data.water.qmmm
Reading data file ...
  orthogonal box = (-6.879301 -6.879301 -6.879301) to (6.879301 6.879301 6.879301)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  6 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  4 bonds
  reading angles ...
  2 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.002 seconds

# QM atoms are 1st water
# MM atoms are 2nd water

group           qm molecule 1
3 atoms in group qm
group           mm molecule 2
3 atoms in group mm

# remove bonds/angles between QM atoms

delete_bonds    qm multi remove special
System init for delete_bonds ...
Deleting bonds ...
  2 total bonds, 2 turned on, 0 turned off
  1 total angles, 1 turned on, 0 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds

# pair style must define stand-alone short-range Coulombics
# must specify mixing explicitly b/c hybrid/overlay
# QM O,H = types 1,2
# MM O,H = types 3,4
# QM O,H atoms do not LJ interact with each other
# only MM O atoms LJ interact with other b/c MM H is zero
# MM/QM O do LJ interact with each other, same as pair of MM O atoms
# MM O and QM H do LJ interact with each other with non-zero H epsilon = 0.044
#   geometric mixing for epsilon, arithmetic for sigma
#   this is to provide stability for QM H atoms

# mixing only for MM-O/QM-O and MM-O/QM-H

pair_style      hybrid/overlay lj/cut 6.0 coul/cut 6.0
pair_coeff      1 1 lj/cut 0.0 3.165558
pair_coeff      2 2 lj/cut 0.0 0.7
pair_coeff      3 3 lj/cut 0.155394 3.165558
pair_coeff      4 4 lj/cut 0.0 0.7
pair_coeff      1 3 lj/cut 0.155394 3.165558
pair_coeff      2 3 lj/cut 0.08268818537130924 1.932779
pair_coeff      * * coul/cut

neighbor	1.0 bin
neigh_modify	delay 0 every 1 check yes

velocity        all create 300.0 87287 loop geom

# QMMM dynamics

timestep        0.1

fix		1 all nve

fix             2 qm mdi/qmmm potential elements O H O H
fix_modify      2 energy yes

thermo_style    custom step cpu temp ke evdwl ecoul epair emol elong                 f_2 pe etotal press

thermo          1
run		10
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 4 4 4
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut, perpetual, skip from (2)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair coul/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
   Step          CPU            Temp          KinEng         E_vdwl         E_coul         E_pair         E_mol          E_long          f_2           PotEng         TotEng         Press     
         0   0              300            4.4712151      0.95937448    -170.68507     -169.7257       3.3962859      0             -10627.88      -10794.209     -10789.738     -296.31483    
         1   16.919228      304.678        4.5409362      0.95696149    -170.42801     -169.47105      3.3391714      0             -10628.16      -10794.292     -10789.751     -305.47131    
         2   34.15349       311.21028      4.6382937      0.9544861     -170.14558     -169.1911       3.25367        0             -10628.467     -10794.404     -10789.766     -318.76873    
         3   51.665217      319.44283      4.7609921      0.9519482     -169.87321     -168.92126      3.1420353      0             -10628.766     -10794.545     -10789.784     -336.5052     
         4   70.038328      329.18599      4.9062046      0.94934821    -169.61529     -168.66594      3.0070837      0             -10629.053     -10794.712     -10789.806     -358.70074    
         5   88.743922      340.2199       5.0706544      0.94668697    -169.37336     -168.42667      2.8521374      0             -10629.326     -10794.901     -10789.83      -385.34191    
         6   106.66884      352.29871      5.2506777      0.94396585    -169.14843     -168.20446      2.6809583      0             -10629.585     -10795.108     -10789.857     -416.40137    
         7   124.39767      365.15522      5.4422918      0.94118664    -168.94159     -168.0004       2.4976729      0             -10629.827     -10795.33      -10789.888     -451.84095    
         8   142.3903       378.50608      5.6412736      0.93835162    -168.75364     -167.81529      2.3066899      0             -10630.053     -10795.562     -10789.921     -491.60675    
         9   159.79847      392.05743      5.8432436      0.93546349    -168.58491     -167.64945      2.1126114      0             -10630.263     -10795.8       -10789.956     -535.62553    
        10   177.34027      405.51042      6.0437477      0.9325254     -168.43613     -167.50361      1.9201417      0             -10630.455     -10796.038     -10789.994     -583.81036    
Loop time of 177.34 on 1 procs for 10 steps with 6 atoms

Performance: 0.000 ns/day, 49261.193 hours/ns, 0.056 timesteps/s, 0.338 atom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.7731e-05 | 6.7731e-05 | 6.7731e-05 |   0.0 |  0.00
Bond    | 3.2954e-05 | 3.2954e-05 | 3.2954e-05 |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 1.9729e-05 | 1.9729e-05 | 1.9729e-05 |   0.0 |  0.00
Output  | 0.00025255 | 0.00025255 | 0.00025255 |   0.0 |  0.00
Modify  | 177.34     | 177.34     | 177.34     |   0.0 |100.00
Other   |            | 2.243e-05  |            |       |  0.00

Nlocal:              6 ave           6 max           6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             56 ave          56 max          56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:             12 ave          12 max          12 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 12
Ave neighs/atom = 2
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:04:02
